Example usage for com.mongodb QueryBuilder get

Introduction

In this page you can find the example usage for com.mongodb QueryBuilder get.

Prototype

public DBObject get() 

Source Link

Document

Creates a DBObject query to be used for the driver's find operations

Usage

From source file:org.opencb.cellbase.mongodb.db.MutationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();

    List<String> ids = new ArrayList<>(regions.size());
    for (Region region : regions) {
        QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("start")
                .greaterThanEquals(region.getStart()).lessThanEquals(region.getEnd());
        queries.add(builder.get());
        ids.add(region.toString());/*from w w  w  . ja v  a 2s  . co  m*/
    }

    return executeQueryList(ids, queries, options);
}

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From source file:org.opencb.cellbase.mongodb.db.network.ProteinProteinInteractionMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult getAll(QueryOptions options) {
    QueryBuilder builder = new QueryBuilder();

    // Fiilter all by interactor ID
    List<Object> interactors = options.getList("interactor", null);
    if (interactors != null && interactors.size() > 0) {
        BasicDBList interactorDBList = new BasicDBList();
        interactorDBList.addAll(interactors);

        BasicDBList or = new BasicDBList();
        DBObject orA = new BasicDBObject("interactorA.xrefs.id", new BasicDBObject("$in", interactorDBList));
        DBObject orB = new BasicDBObject("interactorB.xrefs.id", new BasicDBObject("$in", interactorDBList));
        or.add(orA);//  www.  j  a v  a  2 s.  c o m
        or.add(orB);
        //            builder = builder.or(orA, orB);
        builder = builder.and(new BasicDBObject("$or", or));
    }

    // Filter all by Interaction Type (name and PSIMI)
    List<Object> type = options.getList("type", null);
    if (type != null && type.size() > 0) {
        BasicDBList typeDBList = new BasicDBList();
        typeDBList.addAll(type);

        BasicDBList or = new BasicDBList();
        DBObject orName = new BasicDBObject("type.name", new BasicDBObject("$in", typeDBList));
        DBObject orPsimi = new BasicDBObject("type.psimi", new BasicDBObject("$in", typeDBList));
        or.add(orName);
        or.add(orPsimi);
        //            builder = builder.or(orName, orPsimi);
        builder = builder.and(new BasicDBObject("$or", or));
    }

    // Filter all by source database
    List<Object> database = options.getList("database", null);
    if (database != null && database.size() > 0) {
        BasicDBList databaseDBList = new BasicDBList();
        databaseDBList.addAll(database);
        builder = builder.and("source.name").in(databaseDBList);
    }

    // Filter all by detection method (name and PSIMI)
    List<Object> detectionMethod = options.getList("detectionMethod", null);
    if (detectionMethod != null && detectionMethod.size() > 0) {
        BasicDBList detectionMethodDBList = new BasicDBList();
        detectionMethodDBList.addAll(detectionMethod);

        BasicDBList or = new BasicDBList();
        DBObject orName = new BasicDBObject("detectionMethod.name",
                new BasicDBObject("$in", detectionMethodDBList));
        DBObject orPsimi = new BasicDBObject("detectionMethod.psimi",
                new BasicDBObject("$in", detectionMethodDBList));
        or.add(orName);
        or.add(orPsimi);
        //            builder = builder.or(orName, orPsimi);
        builder = builder.and(new BasicDBObject("$or", or));
    }

    // Filter all by status
    List<Object> status = options.getList("status", null);
    if (status != null && status.size() > 0) {
        BasicDBList statusDBList = new BasicDBList();
        statusDBList.addAll(status);
        builder = builder.and("status").in(statusDBList);
    }

    //        List<Object> type = options.getList("type", null);
    //        if (type != null && type.size() > 0) {
    //            BasicDBList typeDBList = new BasicDBList();
    //            typeDBList.addAll(type);
    //            builder = builder.and("type.name").in(typeDBList);
    //        }

    //        String type = options.getString("type", null);
    //        if (type != null && !type.equals("")) {
    //            builder = builder.and("type.name").is(type);
    //        }

    System.out.println(builder.get().toString());
    //      options = addExcludeReturnFields("transcripts", options);
    return executeQuery("result", builder.get(), options);
}

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From source file:org.opencb.cellbase.mongodb.db.network.ProteinProteinInteractionMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(idList.size());
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("xrefs.id").is(id);
        queries.add(builder.get());
    }/*from  w w  w .  j a va2 s.co m*/
    //        options = addExcludeReturnFields("transcripts", options);
    return executeQueryList(idList, queries, options);
}

---

From source file:org.opencb.cellbase.mongodb.db.ProteinFunctionPredictorMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByEnsemblTranscriptIdList(List<String> transcriptIdList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(transcriptIdList.size());

    if (options.containsKey("aaPosition")) {
        if (options.containsKey("aaChange")) {
            addIncludeReturnFields(/*from   w w  w .ja  va 2  s  .c om*/
                    "aaPositions." + options.getString("aaPosition") + "." + options.getString("aaChange"),
                    options);
        } else {
            addIncludeReturnFields("aaPositions." + options.getString("aaPosition"), options);
        }
    }

    for (String id : transcriptIdList) {
        QueryBuilder builder = QueryBuilder.start("transcriptId").is(id);
        queries.add(builder.get());
    }

    //        options = addExcludeReturnFields("transcripts", options);
    return executeQueryList(transcriptIdList, queries, options);
}

---

From source file:org.opencb.cellbase.mongodb.db.ProteinFunctionPredictorMongoDBAdaptor.java

License:Apache License

public QueryResult getByAaChange(String transcriptId, Integer aaPosition, String newAa,
        QueryOptions queryOptions) {//  w w w.  jav  a 2 s .c o m

    QueryBuilder builder = QueryBuilder.start("transcriptId").is(transcriptId);
    QueryResult allChangesQueryResult = executeQuery(transcriptId, builder.get(), queryOptions);

    QueryResult proteinSubstitionScoresQueryResult = new QueryResult();
    proteinSubstitionScoresQueryResult.setDbTime(allChangesQueryResult.getDbTime());
    proteinSubstitionScoresQueryResult.setId(transcriptId + "-" + aaPosition + "-" + newAa);

    String currentAaShortName;
    Map aaPositions;
    if (allChangesQueryResult.getNumResults() > 0 && (currentAaShortName = aaShortName.get(newAa)) != null
            && (aaPositions = ((HashMap) ((BasicDBObject) allChangesQueryResult.getResult().get(0))
                    .get("aaPositions"))) != null) {
        proteinSubstitionScoresQueryResult.setNumResults(1);
        proteinSubstitionScoresQueryResult.setResult(Arrays.asList(
                ((BasicDBObject) aaPositions.get(Integer.toString(aaPosition))).get(currentAaShortName)));
    } else {
        proteinSubstitionScoresQueryResult.setNumResults(0);
    }

    return proteinSubstitionScoresQueryResult;
}

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From source file:org.opencb.cellbase.mongodb.db.ProteinMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(idList.size());
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("name").is(id);
        queries.add(builder.get());
    }//from w ww  .j a  v  a  2 s.  c o  m

    //        options = addExcludeReturnFields("transcripts", options);
    return executeQueryList(idList, queries, options);
}

---

From source file:org.opencb.cellbase.mongodb.db.regulatory.RegulatoryRegionMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("name").is(id);
        //          System.out.println("Query: " + builder.get());
        queries.add(builder.get());
    }/*from   www.  j av a 2  s. com*/
    //        options = addExcludeReturnFields("chunkIds", options);
    return executeQueryList2(idList, queries, options);
}

---

From source file:org.opencb.cellbase.mongodb.db.regulatory.RegulatoryRegionMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByPositionList(List<Position> positionList, QueryOptions options) {
    //  db.regulatory_region.find({"chunkIds": {$in:["1_200", "1_300"]}, "start": 601156})

    String featureType = options.getString("featureType", null);
    String featureClass = options.getString("featureClass", null);

    List<DBObject> queries = new ArrayList<>();
    for (Position position : positionList) {
        String chunkId = position.getChromosome() + "_"
                + getChunkId(position.getPosition(), regulatoryRegionChunkSize) + "_"
                + regulatoryRegionChunkSize / 1000 + "k";
        BasicDBList chunksId = new BasicDBList();
        chunksId.add(chunkId);/*  www  .  ja  v  a  2s .  com*/
        QueryBuilder builder = QueryBuilder.start("_chunkIds").in(chunksId).and("start")
                .is(position.getPosition());
        if (featureType != null) {
            builder.and("featureType").is(featureType);
        }
        if (featureClass != null) {
            builder.and("featureClass").is(featureClass);
        }

        //        System.out.println("Query: " + builder.get());
        queries.add(builder.get());
    }

    System.out.println("Query: " + queries);

    //        options = addExcludeReturnFields("chunkIds", options);
    return executeQueryList2(positionList, queries, options);
}

---

From source file:org.opencb.cellbase.mongodb.db.regulatory.RegulatoryRegionMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByRegionList(List<Region> regionList, QueryOptions options) {
    //  db.regulatory_region.find({"chunkIds": {$in:["1_200", "1_300"]}, "start": 601156})
    QueryBuilder builder = new QueryBuilder();

    List<Object> featureType = options.getAsList("featureType");
    List<Object> featureClass = options.getAsList("featureClass");

    //        options = addExcludeReturnFields("chunkIds", options);

    List<DBObject> queries = new ArrayList<>();
    for (Region region : regionList) {
        int firstChunkId = getChunkId(region.getStart(), regulatoryRegionChunkSize);
        int lastChunkId = getChunkId(region.getEnd(), regulatoryRegionChunkSize);
        BasicDBList chunksId = new BasicDBList();
        for (int j = firstChunkId; j <= lastChunkId; j++) {
            String chunkId = region.getChromosome() + "_" + j + "_" + regulatoryRegionChunkSize / 1000 + "k";
            chunksId.add(chunkId);//from w  ww .  j a  va 2s  .  c  o  m
        }

        //            logger.info(chunksId.toString());

        builder = builder.start("_chunkIds").in(chunksId).and("start").lessThanEquals(region.getEnd())
                .and("end").greaterThanEquals(region.getStart());

        if (featureType != null && featureType.size() > 0) {
            BasicDBList featureTypeDBList = new BasicDBList();
            featureTypeDBList.addAll(featureType);
            builder = builder.and("featureType").in(featureTypeDBList);
        }

        if (featureClass != null && featureClass.size() > 0) {
            BasicDBList featureClassDBList = new BasicDBList();
            featureClassDBList.addAll(featureClass);
            builder = builder.and("featureClass").in(featureClassDBList);
        }

        queries.add(builder.get());
    }
    //        System.out.println(">>"+regionList);
    //        System.out.println(">>"+builder.get().toString());
    return executeQueryList2(regionList, queries, options);
}

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From source file:org.opencb.cellbase.mongodb.db.regulatory.RegulatoryRegionMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult next(String chromosome, int position, QueryOptions options) {

    String featureType = options.getString("featureType", null);
    String featureClass = options.getString("featureClass", null);

    BasicDBList chunksId = new BasicDBList();
    String chunkId = chromosome + "_" + getChunkId(position, regulatoryRegionChunkSize) + "_"
            + regulatoryRegionChunkSize / 1000 + "k";
    chunksId.add(chunkId);/* w  ww  .  j  a v  a  2  s . c  om*/

    // TODO: Add query to find next item considering next chunk
    // db.regulatory_region.find({ "chromosome" : "19" , "start" : { "$gt" : 62005} , "featureType" : "TF_binding_site_motif"}).sort({start:1}).limit(1)

    QueryBuilder builder;
    if (options.getString("strand") == null
            || (options.getString("strand").equals("1") || options.getString("strand").equals("+"))) {
        // db.core.find({chromosome: "1", start: {$gt: 1000000}}).sort({start: 1}).limit(1)
        builder = QueryBuilder.start("_chunkIds").in(chunksId).and("chromosome").is(chromosome).and("start")
                .greaterThan(position);
        options.put("sort", new BasicDBObject("start", 1));
        options.put("limit", 1);
    } else {
        builder = QueryBuilder.start("_chunkIds").in(chunksId).and("chromosome").is(chromosome).and("end")
                .lessThan(position);
        options.put("sort", new BasicDBObject("end", -1));
        options.put("limit", 1);
    }

    if (featureType != null) {
        builder.and("featureType").is(featureType);
    }
    if (featureClass != null) {
        builder.and("featureClass").is(featureClass);
    }
    System.out.println(builder.get());
    return executeQuery("result", builder.get(), options);
}

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